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Yorodumi- EMDB-60098: pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV -
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Open data
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Basic information
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| Title | pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV | |||||||||
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Keywords | 80S ribosome / RIBOSOME | |||||||||
| Function / homology | Function and homology informationRNA 5'-cap (guanine-N7)-methylation / RNA stabilization / translation termination factor activity / DNA/DNA annealing activity / translation release factor complex / cytoplasmic translational termination / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / RNA strand annealing activity / regulation of translational termination / RNA folding chaperone ...RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / translation termination factor activity / DNA/DNA annealing activity / translation release factor complex / cytoplasmic translational termination / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / RNA strand annealing activity / regulation of translational termination / RNA folding chaperone / symbiont-mediated suppression of host apoptosis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / translation release factor activity, codon specific / protein methylation / translation release factor activity / regulation of amino acid metabolic process / negative regulation of glucose mediated signaling pathway / positive regulation of translational fidelity / Negative regulators of DDX58/IFIH1 signaling / sequence-specific mRNA binding / RMTs methylate histone arginines / Protein methylation / peptidyl-tRNA hydrolase activity / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / response to cycloheximide / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of mRNA splicing, via spliceosome / positive regulation of protein kinase activity / negative regulation of translational frameshifting / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome, large subunit precursor / Protein hydroxylation / Formation of a pool of free 40S subunits / flavivirin / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational elongation / Eukaryotic Translation Termination / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / G-protein alpha-subunit binding / ribosomal large subunit export from nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / 90S preribosome / Ub-specific processing proteases / positive regulation of viral genome replication / protein-RNA complex assembly / regulation of translational fidelity / translational termination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / ribosomal subunit export from nucleus / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / ribosomal small subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / cytosolic ribosome / rescue of stalled cytosolic ribosome / protein kinase C binding / cellular response to amino acid starvation / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / macroautophagy / small-subunit processome / translational initiation / protein-DNA complex / maintenance of translational fidelity / modification-dependent protein catabolic process / Regulation of expression of SLITs and ROBOs / protein tag activity / cytoplasmic stress granule / rRNA processing / viral capsid / peptidase activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly Similarity search - Function | |||||||||
| Biological species | ![]() ![]() West Nile virus / Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
Authors | Wu M / Yuan S | |||||||||
| Funding support | China, 1 items
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Citation | Journal: To Be PublishedTitle: Flexibilities and conservations in the structural basis of viral -1 programmed ribosomal frameshifting Authors: Wu M / Wan X / Zhou H / Yuan S | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_60098.map.gz | 778.9 MB | EMDB map data format | |
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| Header (meta data) | emd-60098-v30.xml emd-60098.xml | 100.1 KB 100.1 KB | Display Display | EMDB header |
| Images | emd_60098.png | 67.4 KB | ||
| Filedesc metadata | emd-60098.cif.gz | 18.6 KB | ||
| Others | emd_60098_half_map_1.map.gz emd_60098_half_map_2.map.gz | 764.5 MB 764.5 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-60098 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-60098 | HTTPS FTP |
-Validation report
| Summary document | emd_60098_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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| Full document | emd_60098_full_validation.pdf.gz | 1 MB | Display | |
| Data in XML | emd_60098_validation.xml.gz | 20.2 KB | Display | |
| Data in CIF | emd_60098_validation.cif.gz | 24.4 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60098 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60098 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8zhcMC ![]() 8zgrC ![]() 8zgyC ![]() 8zh3C ![]() 8zhbC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_60098.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.95 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #2
| File | emd_60098_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_60098_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : 80S ribosome
+Supramolecule #1: 80S ribosome
+Macromolecule #1: 25S rRNA (3393-MER)
+Macromolecule #2: 5S rRNA (121-MER)
+Macromolecule #3: 5.8S rRNA (158-MER)
+Macromolecule #45: chain 2 18S rRNA (1799-MER)
+Macromolecule #79: tRNA (77-MER)
+Macromolecule #81: RNA (5'-R(P*GP*AP*CP*CP*CP*UP*UP*AP*AP*C)-3')
+Macromolecule #4: Large ribosomal subunit protein uL2A
+Macromolecule #5: Large ribosomal subunit protein uL3
+Macromolecule #6: Large ribosomal subunit protein uL4A
+Macromolecule #7: Large ribosomal subunit protein uL18
+Macromolecule #8: Large ribosomal subunit protein eL6B
+Macromolecule #9: Large ribosomal subunit protein uL30A
+Macromolecule #10: Large ribosomal subunit protein eL8A
+Macromolecule #11: Large ribosomal subunit protein uL6A
+Macromolecule #12: Large ribosomal subunit protein uL16
+Macromolecule #13: Large ribosomal subunit protein uL5B
+Macromolecule #14: Large ribosomal subunit protein eL13A
+Macromolecule #15: Large ribosomal subunit protein eL14A
+Macromolecule #16: Large ribosomal subunit protein eL15A
+Macromolecule #17: Large ribosomal subunit protein uL13A
+Macromolecule #18: Large ribosomal subunit protein uL22A
+Macromolecule #19: Large ribosomal subunit protein eL18A
+Macromolecule #20: Large ribosomal subunit protein eL19A
+Macromolecule #21: Large ribosomal subunit protein eL20A
+Macromolecule #22: Large ribosomal subunit protein eL21A
+Macromolecule #23: Large ribosomal subunit protein eL22A
+Macromolecule #24: Large ribosomal subunit protein uL14A
+Macromolecule #25: Large ribosomal subunit protein eL24A
+Macromolecule #26: Large ribosomal subunit protein uL23
+Macromolecule #27: Large ribosomal subunit protein uL24A
+Macromolecule #28: Large ribosomal subunit protein eL27A
+Macromolecule #29: Large ribosomal subunit protein uL15
+Macromolecule #30: Large ribosomal subunit protein eL29
+Macromolecule #31: Large ribosomal subunit protein eL30
+Macromolecule #32: Large ribosomal subunit protein eL31A
+Macromolecule #33: Large ribosomal subunit protein eL32
+Macromolecule #34: Large ribosomal subunit protein eL33A
+Macromolecule #35: Large ribosomal subunit protein eL34A
+Macromolecule #36: Large ribosomal subunit protein uL29A
+Macromolecule #37: Large ribosomal subunit protein eL36A
+Macromolecule #38: Large ribosomal subunit protein eL37A
+Macromolecule #39: Large ribosomal subunit protein eL38
+Macromolecule #40: Large ribosomal subunit protein eL39
+Macromolecule #41: Large ribosomal subunit protein eL40A
+Macromolecule #42: Large ribosomal subunit protein eL41A
+Macromolecule #43: Large ribosomal subunit protein eL42A
+Macromolecule #44: Large ribosomal subunit protein eL43A
+Macromolecule #46: Small ribosomal subunit protein uS3
+Macromolecule #47: Small ribosomal subunit protein uS7
+Macromolecule #48: Small ribosomal subunit protein eS10A
+Macromolecule #49: Small ribosomal subunit protein eS12
+Macromolecule #50: Small ribosomal subunit protein uS19
+Macromolecule #51: Small ribosomal subunit protein uS9A
+Macromolecule #52: Small ribosomal subunit protein eS17A
+Macromolecule #53: Small ribosomal subunit protein uS13A
+Macromolecule #54: Small ribosomal subunit protein eS19A
+Macromolecule #55: Small ribosomal subunit protein uS10
+Macromolecule #56: Small ribosomal subunit protein eS25A
+Macromolecule #57: Small ribosomal subunit protein eS28A
+Macromolecule #58: Small ribosomal subunit protein uS14A
+Macromolecule #59: Small ribosomal subunit protein eS31
+Macromolecule #60: Small ribosomal subunit protein RACK1
+Macromolecule #61: Small ribosomal subunit protein uS2A
+Macromolecule #62: Small ribosomal subunit protein eS1A
+Macromolecule #63: Small ribosomal subunit protein uS5
+Macromolecule #64: Small ribosomal subunit protein eS4A
+Macromolecule #65: Small ribosomal subunit protein eS6A
+Macromolecule #66: Small ribosomal subunit protein eS7A
+Macromolecule #67: Small ribosomal subunit protein eS8A
+Macromolecule #68: Small ribosomal subunit protein uS4A
+Macromolecule #69: Small ribosomal subunit protein uS17A
+Macromolecule #70: Small ribosomal subunit protein uS15
+Macromolecule #71: Small ribosomal subunit protein uS11B
+Macromolecule #72: Small ribosomal subunit protein eS21A
+Macromolecule #73: Small ribosomal subunit protein uS8A
+Macromolecule #74: Small ribosomal subunit protein uS12A
+Macromolecule #75: Small ribosomal subunit protein eS24A
+Macromolecule #76: Small ribosomal subunit protein eS26B
+Macromolecule #77: Small ribosomal subunit protein eS27A
+Macromolecule #78: Small ribosomal subunit protein eS30A
+Macromolecule #80: Eukaryotic peptide chain release factor subunit 1
+Macromolecule #82: Peptide 2k
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | JEOL CRYO ARM 300 |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
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About Yorodumi



Keywords
West Nile virus
Homo sapiens (human)
Authors
China, 1 items
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Processing
FIELD EMISSION GUN